Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-01-28 11:05:42 -0500 (Sat, 28 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4465
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4246
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4269
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for karyoploteR on nebbiolo1


To the developers/maintainers of the karyoploteR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/karyoploteR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1004/2162HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
karyoploteR 1.25.0  (landing page)
Bernat Gel
Snapshot Date: 2023-01-27 14:00:19 -0500 (Fri, 27 Jan 2023)
git_url: https://git.bioconductor.org/packages/karyoploteR
git_branch: master
git_last_commit: 051aa8b
git_last_commit_date: 2022-11-01 11:15:07 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    NA  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: karyoploteR
Version: 1.25.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings karyoploteR_1.25.0.tar.gz
StartedAt: 2023-01-27 21:24:27 -0500 (Fri, 27 Jan 2023)
EndedAt: 2023-01-27 21:32:35 -0500 (Fri, 27 Jan 2023)
EllapsedTime: 488.3 seconds
RetCode: 0
Status:   OK  
CheckDir: karyoploteR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings karyoploteR_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/karyoploteR.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.25.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘karyoploteR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘regioneR’ ‘GenomicRanges’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
kpPlotDensity     32.364  6.808  39.246
kpPlotGenes       21.285  0.792  22.079
mergeTranscripts  16.078  0.134  16.212
kpPlotHorizon     14.783  0.283  15.067
kpPlotRegions     12.296  0.348  12.644
kpPlotBAMCoverage  7.255  0.496   7.752
kpPlotTranscripts  5.946  0.052   5.998
kpPlotManhattan    5.203  0.108   5.310
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘karyoploteR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.



Installation output

karyoploteR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL karyoploteR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘karyoploteR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (karyoploteR)

Tests output

karyoploteR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(karyoploteR)
Loading required package: regioneR
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> test_check("karyoploteR")
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 181 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 181 ]
> 
> proc.time()
   user  system elapsed 
 18.080   0.918  18.986 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames2.5960.1602.756
autotrack0.0010.0010.001
colByCategory0.0020.0000.003
colByChr0.4660.0030.470
colByRegion1.0320.1241.157
colByValue0.1750.0050.180
darker0.0010.0000.001
filterParams0.0010.0000.000
findIntersections0.1080.0070.115
getChromosomeNamesBoundingBox0.0430.0010.042
getColorSchemas0.0000.0030.003
getCytobandColors0.0020.0000.001
getCytobands0.0010.0010.001
getDataPanelBoundingBox0.0390.0000.039
getDefaultPlotParams0.0630.0070.070
getMainTitleBoundingBox0.0300.0010.029
getTextSize0.0710.0000.070
getVariantsColors0.0010.0000.001
horizonColors0.0040.0000.003
is.color0.0010.0000.000
kpAbline2.0290.1952.227
kpAddBaseNumbers0.3290.0200.348
kpAddChromosomeNames0.0250.0040.030
kpAddChromosomeSeparators0.4050.0070.413
kpAddColorRect0.1350.0000.135
kpAddCytobandLabels0.3910.0200.411
kpAddCytobands0.0300.0050.036
kpAddCytobandsAsLine0.0590.0120.070
kpAddLabels0.4180.0160.435
kpAddMainTitle0.0290.0000.028
kpArea0.3300.0120.342
kpArrows0.5200.0560.575
kpAxis0.3050.0280.332
kpBars0.1810.0000.180
kpDataBackground0.1960.0080.204
kpHeatmap0.1360.0040.141
kpLines0.2480.0040.252
kpPlotBAMCoverage7.2550.4967.752
kpPlotBAMDensity1.8690.0201.888
kpPlotBigWig0.8700.0360.907
kpPlotCoverage0.4330.0160.449
kpPlotDensity32.364 6.80839.246
kpPlotGenes21.285 0.79222.079
kpPlotHorizon14.783 0.28315.067
kpPlotLinks1.1730.0241.199
kpPlotLoess0.0700.0000.071
kpPlotManhattan5.2030.1085.310
kpPlotMarkers1.6100.0201.631
kpPlotNames0.110.000.11
kpPlotRainfall0.7730.0150.788
kpPlotRegions12.296 0.34812.644
kpPlotRibbon0.0840.0000.085
kpPlotTranscripts5.9460.0525.998
kpPoints0.2700.0200.289
kpPolygon0.1980.0080.206
kpRect0.6740.0200.693
kpSegments0.5460.0120.558
kpText0.2360.0040.239
lighter0.0010.0000.001
makeGenesDataFromTxDb3.1000.1043.205
mergeTranscripts16.078 0.13416.212
plotDefaultPlotParams0.1580.0000.158
plotKaryotype0.9590.0641.022
plotPalettes0.0150.0040.019
prepareParameters20.0360.0000.036
prepareParameters40.0290.0040.033
processClipping0.0320.0000.032
transparent0.0010.0000.001